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I am trying to perform Meta-analysis to verify the quality of micro-array studies. I have a list of two studies with eight samples in each.
testdf $agaz 1 1 1 1 2 2 2 2 ID 1.00000 2.00000 1.0000000 2.00000 1.0000000 2.00000 1.0000000 2.00000 SLC20A1 3242.90209 3242.90209 242.9020870 3242.90209 242.9020870 3242.90209 242.9020870 3242.90209 PRDX4 377.81481 377.81481 77.8148132 377.81481 77.8148132 377.81481 77.8148132 377.81481 MCM6 114.88743 114.88743 14.8874270 114.88743 14.8874270 114.88743 14.8874270 114.88743 HEXB 8739.03257 8739.03257 739.0325730 8739.03257 739.0325730 8739.03257 739.0325730 8739.03257 CCT2 60.73464 60.73464 0.7346439 60.73464 0.7346439 60.73464 0.7346439 60.73464 ALCAM 821.84659 821.84659 21.8465904 821.84659 21.8465904 821.84659 21.8465904 821.84659 EGFR 144.62966 144.62966 44.6296574 144.62966 44.6296574 144.62966 44.6296574 144.62966 DDR1 254.37172 254.37172 54.3717175 254.37172 54.3717175 254.37172 54.3717175 254.37172 RFC2 84.09299 84.09299 4.0929930 84.09299 4.0929930 84.09299 4.0929930 84.09299 HSPA6 57.67287 57.67287 7.6728694 57.67287 7.6728694 57.67287 7.6728694 57.67287 PAX8 78.58733 78.58733 78.8733051 78.58733 78.8733051 78.58733 78.8733051 78.58733 GUCA1A 260.99620 260.99620 200.9962012 260.99620 200.9962012 260.99620 200.9962012 260.99620 UBA7 141.73193 141.73193 41.7319334 141.73193 41.7319334 141.73193 41.7319334 141.73193 THRA 714.82358 714.82358 704.8235783 714.82358 704.8235783 714.82358 704.8235783 714.82358 PTPN21 293.68721 293.68721 293.6872066 293.68721 293.6872066 293.68721 293.6872066 293.68721 CCL5 3242.90209 3242.90209 3242.9020870 3242.90209 3242.9020870 3242.90209 3242.9020870 3242.90209 CYP2E1 57.67287 57.67287 57.6728694 57.67287 57.6728694 57.67287 57.6728694 57.67287 EPHB3 57.67287 57.67287 57.6728694 57.67287 57.6728694 57.67287 57.6728694 57.67287 $hussain 1 1 2 2 2 2 1 1 ID 1.00000 2.00000 1.00000 2.00000 1.00000 2.00000 1.00000 2.00000 SLC20A1 3242.90209 3242.90209 3242.90209 3242.90209 3242.90209 3242.90209 3242.90209 3242.90209 PRDX4 377.81481 377.81481 377.81481 377.81481 377.81481 377.81481 377.81481 377.81481 MCM6 114.88743 114.88743 114.88743 114.88743 114.88743 114.88743 114.88743 114.88743 HEXB 8739.03257 8739.03257 8739.03257 8739.03257 8739.03257 8739.03257 8739.03257 8739.03257 CCT2 60.73464 60.73464 60.73464 60.73464 60.73464 60.73464 60.73464 60.73464 ALCAM 821.84659 821.84659 821.84659 821.84659 821.84659 821.84659 821.84659 821.84659 EGFR 144.62966 144.62966 144.62966 144.62966 144.62966 144.62966 144.62966 144.62966 DDR1 254.37172 254.37172 254.37172 254.37172 254.37172 254.37172 254.37172 254.37172 RFC2 84.09299 84.09299 84.09299 84.09299 84.09299 84.09299 84.09299 84.09299 HSPA6 57.67287 57.67287 57.67287 57.67287 57.67287 57.67287 57.67287 57.67287 PAX8 78.58733 78.58733 78.58733 78.58733 78.58733 78.58733 78.58733 78.58733 GUCA1A 260.99620 260.99620 260.99620 260.99620 260.99620 260.99620 260.99620 260.99620 UBA7 141.73193 141.73193 141.73193 141.73193 141.73193 141.73193 141.73193 141.73193 THRA 714.82358 714.82358 714.82358 714.82358 714.82358 714.82358 714.82358 714.82358 PTPN21 293.68721 293.68721 293.68721 293.68721 293.68721 293.68721 293.68721 293.68721 CCL5 3242.90209 3242.90209 3242.90209 3242.90209 3242.90209 3242.90209 3242.90209 3242.90209 CYP2E1 57.67287 57.67287 57.67287 57.67287 57.67287 57.67287 57.67287 57.67287 EPHB3 57.67287 57.67287 57.67287 57.67287 57.67287 57.67287 57.67287 57.67287
I run the following code :
testdfQC <- MetaQC(testdf, "c2.cp.biocarta.v5.0.symbols.gmt", filterGenes=FALSE, verbose=TRUE, isParallel=TRUE, nCores=4)
But I get
Error in { : task 1 failed - "!is.null(d$y) && !is.null(colnames(d$x)) is not TRUE"
No idea what is going wrong. Help appreciated.
I don't think MetaQC is a Bioconductor package so you should contact its maintainer.